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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACTGAACCGTCAGGTTGTGAAATCTGATTCAGCAACTATTAAGgtatgtcaaactatgctcttgtgatgctttttaaatatatgtaatgtgatttatatgtaacttcacatttgacgtgtag

Basic information

species Oryza sativa
transcript LOC_Os08g36774.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g36774.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G351582_T01 (Zea mays), 5'ss of exon 6
ATACTGAACCGTCAGGTTGTGAAATCTGATTCAGCAACTATTAAGgtatgtcaaactatgctc-ttgtgatgctttt---taaatatatgtaatgtgatttatatgtaacttcacatttgacgtgtag----
|| ||||| |||||||| ||||| ||||||||||| ||||| |||||||| | | || || | |||| | | |||||| || |||| | | | ||||| |||| || |
ATGCTGAATCGTCAGGTCGTGAAGTCTGATTCAGCGACTATCAAGgtatgctgatatttgatcatcttgatacatcacagtaaatacattgaatgcattgcttttctaactattcattgtacccatctgcag
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|58683822|gb|CK072509.1|CK072509
EST:     ATACTGAACCGTCAGGTTGTGAAATCTGATTCAGCAACTATTAAG                         ATTCCAGAACTGGACTTTGAGATCCCTCCAGAAGCTCAACGTGGATCACTT
genomic: ATACTGAACCGTCAGGTTGTGAAATCTGATTCAGCAACTATTAAGgtatgtcaaa ... tgacgtgtagATTCCAGAACTGGACTTTGAGATCCCTCCAGAAGCTCAACGTGGATCACTT
EST: gi|29686073|gb|CB682348.1|CB682348
EST:     ATACTGAACCGTCAGGTTGTGAAATCTGATTCAGCAACTATTAAG                         ATTCCAGAACTGGACTTTGAGATCCCTCCAGAAGCTCAACGTGGATCACTT
genomic: ATACTGAACCGTCAGGTTGTGAAATCTGATTCAGCAACTATTAAGgtatgtcaaa ... tgacgtgtagATTCCAGAACTGGACTTTGAGATCCCTCCAGAAGCTCAACGTGGATCACTT
EST: gi|218499091|gb|FG956697.1|FG956697
EST:     ATACTGAACCGTCAGGTTGTGAAATCTGATTCAGCAACTATTAAG                         ATTCCAGAACTGGACTTTGAGATCCCTCCAGAAGCTCAACGTGGATCACTT
genomic: ATACTGAACCGTCAGGTTGTGAAATCTGATTCAGCAACTATTAAGgtatgtcaaa ... tgacgtgtagATTCCAGAACTGGACTTTGAGATCCCTCCAGAAGCTCAACGTGGATCACTT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 74 (upstream exon), 71 (downstream exon)
Score: 22

ATACTGAACCGTCAGGTTGTGAAATCTGATTCAGCAACTATTAAGgtatgtcaaa ... tgacgtgtagATTCCAGAACTGGACTTTGAGATCCCTCCAGAAGCTCAACGTGGATCACTTTCAACA




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